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  • 1.
    Aliyu, Habibu
    et al.
    Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.
    De Maayer, Pieter
    School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Cowan, Donald A.
    Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.
    Metagenomic Analysis of Low-Temperature Environments2017Ingår i: Psychrophiles: From Biodiversity to Biotechnology / [ed] Rosa Margesin, Cham: Springer, 2017, s. 389-421Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    The Earth’s permanently cold biosphere is known to harbour abundant microbial biomass and represents a rich resource for the discovery of novel cold-adapted microorganisms, many of which form part of the ‘microbial dark matter’ which cannot be analysed using traditional culture-dependent approaches. The recent development of metagenomics and related multi-omics strategies has provided a means by which entire microbial communities can be studied directly, without the prerequisite of culturing. The advancement of the ‘omic’ methods is directly linked to recent progress in high-throughput sequencing, robust data processing capabilities and the application of cutting-edge analytical tools for high-throughput detection of biomolecules. The combined application of these tools and strategies has provided an unprecedented access to the structure and potential function of microbial communities in cold environments, providing increasingly comprehensive insights into the taxonomic richness and functional capacity of the indigenous microorganisms. Applications of ‘omic’ strategies have enhanced our understanding of psychrophilic adaptation mechanisms, revealing the versatility and adaptability of life in the ‘cryosphere’. In addition to the predicted roles of psychrophiles in biogeochemical cycling, recent multi-omic studies have further emphasised the importance of the ‘cryosphere’ in influencing global atmospheric conditions. Finally, metagenomic bioprospecting of cold environments has yielded a variety of novel bioactive molecules including novel ‘psychrozymes’, with a wide range of potential industrial and biotechnological applications. Here, we have provided an overview of recent developments in metagenomic technologies and their application in the study of the cold biosphere.

  • 2.
    Berini, Francesca
    et al.
    Politecnico di Milano and University of Insubria, Varese, Italy.
    Presti, Ilaria
    Politecnico di Milano and University of Insubria, Varese, Italy / Chemo Biosynthesis, Corana, Pavia, Italy.
    Beltrametti, Fabrizio
    Actygea, Gerenzano, Varese, Italy.
    Pedroli, Marco
    Vårum, Kjell M
    Norwegian University of Science and Technology, Trondheim, Norway.
    Pollegioni, Loredano
    Politecnico di Milano and University of Insubria, Varese, Italy.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Marinelli, Flavia
    Politecnico di Milano and University of Insubria, Varese, Italy.
    Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome2017Ingår i: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 16, nr 1, artikel-id 16Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND: Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase-named Chi18H8 and belonging to family 18 glycosyl hydrolases-was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential.

    RESULTS: We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca(2+)-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate.

    CONCLUSIONS: Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies.

  • 3.
    Dalusi, Lucy
    et al.
    Amana Regional Referral Hospital, Dar es Salaam, Tanzania / University of Dar es Salaam, Dar es Salaam, Tanzania.
    Lyimo, Thomas J
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Lugomela, Charles
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Hosea, Ken M M
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Toxigenic Vibrio cholerae identified in estuaries of Tanzania using PCR techniques2015Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 362, nr 5, artikel-id fnv009Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in environmental samples along salinity gradients in three selected estuaries of Tanzania both through culture independent methods and by cultured bacteria. Occurrence of V. cholerae was determined by PCR targeting the V. cholerae outer membrane protein gene ompW. Furthermore, the presence of toxigenic strains and serogroups O1 and O139 was determined using multiplex PCR with specific primers targeting the cholera toxin gene subunit A, ctxA, and serotype specific primers, O1-rfb and O139-rfb, respectively. Results showed that V. cholerae occurred in approximately 10% (n = 185) of both the environmental samples and isolated bacteria. Eight of the bacteria isolates (n = 43) were confirmed as serogroup O1 while one belonged to serogroup O139, the first reported identification of this epidemic strain in East African coastal waters. All samples identified as serogroup O1 or O139 and a number of non-O1/O139 strains were ctxA positive. This study provides in situ evidence of the presence of pathogenic V. cholerae O1 and O139 and a number of V. cholerae non-O1/O139 that carry the cholera toxin gene in estuaries along the coast of Tanzania.

  • 4.
    Dealtry, Simone
    et al.
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    Ding, Guo-Chun
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    Weichelt, Viola
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
    Dunon, Vincent
    ivision of Soil and Water Management, KU Leuven, Heverlee, Belgium .
    Schlüter, Andreas
    Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany.
    Martini, María Carla
    BBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina .
    Papa, María Florencia Del
    IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina .
    Lagares, Antonio
    IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
    Amos, Gregory Charles Auton
    School of Life Sciences, University of Warwick, Warwick, United Kingdom .
    Wellington, Elizabeth Margaret Helen
    chool of Life Sciences, University of Warwick, Warwick, United Kingdom .
    Gaze, William Hugo
    School of Life Sciences, University of Warwick, Warwick, United Kingdom .
    Sipkema, Detmer
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands .
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Springael, Dirk
    Division of Soil and Water Management, KU Leuven, Heverlee, Belgium.
    Heuer, Holger
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    van Elsas, Jan Dirk
    University of Groningen, Groningen, The Netherlands .
    Thomas, Christopher
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, Warwick, United Kingdom .
    Smalla, Kornelia
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats.2014Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 2, artikel-id e89922Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.

  • 5.
    Dionisi, Hebe
    et al.
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Matos, Marina
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Anselmino, Luciano
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Lozada, Mariana
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Mac Cormack, Walter
    Argentinean Antarctic Inst, Buenos Aires, DF, Argentina / Natl Univ Buenos Aires, Buenos Aires, DF, Argentina.
    Carroll, Jolynn
    Univ Tromsö, N-9001 Tromsö, Norway / Akvaplan Niva AS, FRAM High North Res Ctr Climate & Environm, Tromsö, Norway.
    Lundgren, Leif
    Stockholm University.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Chavarria, Krystle
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Henrissat, Bernard
    Ctr Natl Rech Sci, Marseille, France.
    Jansson, Janet
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Mining alginate lyases in sediment metagenomes from four geographically distant cold coastal environments2014Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, s. S69-S70Artikel i tidskrift (Refereegranskat)
  • 6.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Hårdeman, Fredrik
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska institutet.
    Jansson, Janet K.
    SLU / Lawrence Berkeley National Laboratory, Berkeley, USA.
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Active bacterial community structure along vertical redox gradients in Baltic Sea sediment2008Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, nr 8, s. 2051-2063Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, -64 and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  • 7.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Soule, T
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Jansson, J K
    Microbial community structure in polluted Baltic Sea sediments2006Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 8, nr 2, s. 223-232Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nearly half the seabed of the Baltic Proper is incapable of supporting life of higher organisms as a consequence of oxygen depletion resulting from eutrophication. However, these areas are actually teeming with microbial life. Here we used terminal-restriction fragment length polymorphism (T-RFLP) to investigate the dominant archaeal and bacterial groups, with respect to community structure, in surface layers of bottom sediments of the Baltic Sea along a coastal pollution gradient. Both archaeal and bacterial communities formed distinct clusters along the pollution gradient and the community compositions were different at the polluted sites compared with the relatively clean reference sites. The structures of the bacterial communities were most strongly correlated to water depth, followed by organic carbon, oxygen, salinity and silicate levels. In contrast, the structures of the archaeal communities were most strongly correlated to oxygen, salinity, organic carbon, silicate and nitrate levels. Some members of the microbial communities were identified using a combination of traditional and molecular approaches. Isolates obtained on different culture media were identified by partial sequencing of their 16S rRNA genes and some novel species were found. In addition, we developed a computer program, APLAUS, to elucidate the putative identities of the most dominant community members by T-RFLP.

  • 8. Engel, Katja
    et al.
    Ashby, Deborah
    Brady, Sean F.
    Cowan, Don A.
    Doemer, John
    Edwards, Elizabeth A.
    Fiebig, Klaus
    Martens, Eric C.
    McCormac, Dennis
    Mead, David A.
    Miyazaki, Kentaro
    Moreno-Hagelsieb, Gabriel
    O'Gara, Fergal
    Reid, Alexandra
    Rose, David R.
    Simonet, Pascal
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Smalla, Kornelia
    Streit, Wolfgang R.
    Tedman-Jones, Jennifer
    Valla, Svein
    Wellington, Elizabeth M. H.
    Wu, Cheng-Cang
    Liles, Mark R.
    Neufeld, Josh D.
    Sessitsch, Angela
    Charles, Trevor C.
    Meeting Report: 1st International Functional Metagenomics Workshop May 7-8, 2012, St. Jacobs, Ontario, Canada2013Ingår i: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 8, nr 1, s. 106-111Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.

  • 9. Eriksson, AnnaCarin
    et al.
    Glaser, Elzbieta
    Sjöling, Sara
    A general processing proteinase of spinach leaf mitochondria is a membrane bound enzyme1993Ingår i: Plant Mitochondria: with emphasis on RNA editing and cytoplasmic male sterility / [ed] Brennicke, Axel and Kuch, U, VCH Verlag , 1993, s. 233-241Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    The book summarizes our current knowledge in the molecular biology of plant mitochondria. It covers such topics as: - RNA editing - mitochondrial gene organization and expression - protein synthesis and transport - cytoplasmic male sterility Specific emphasis is placed on RNA editing. Different systems known to date in mitochondria and plastids are compared. In addition, their connection with the molecular biology involved with the functional analysis is delineated. Another major topic is the molecular biology of mitochondrial genomes of cytoplasmic male sterile (cms) plants. The similarities observed in different cms systems not only promote our understanding of those processes which lead to male sterile plants but are also helpful for breeding strategies. Concise and timely, this book is a unique collaboration of researchers from different fields.

  • 10. Eriksson, AnnaCarin
    et al.
    Sjöling, Sara
    Glaser, Elzbieta
    Characterization of the bifunctional mitochondrial processing peptidase (MPP)/bc1 complex in Spinacia oleracea1996Ingår i: Journal of Bioenergetics and Biomembranes, ISSN 0145-479X, E-ISSN 1573-6881, Vol. 28, nr 3, s. 285-292Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The mitochondrial general processing peptidase (MPP) in plant mitochondria constitutes an integral part of the cytochromebc 1 complex of the respiratory chain. Here we present a characterization of this bifunctional complex from spinach leaf mitochondria. The purified MPP/bc 1 complex has a molecular mass of 550 kDa, which corresponds to a dimer. Increased ionic strength results in partial dissociation of the dimer as well as loss of the processing activity. Micellar concentrations of nonionic and zwitterionic detergents stimulate the activity by decreasing the temperature optimum of the processing reaction, whereas anionic detergents totally suppress the activity. MPP is a metalloendopeptidase. Interestingly, hemin, a potent regulator of mitochondrial and cytosolic biogenesis and inhibitor of proteosomal degradation, inhibits the processing activity. Measurements of the processing activity at different redox states of the bc 1 complex show that despite bifunctionality of the MPP/bc 1 complex, there is no correlation between electron transfer and protein processing.

  • 11.
    Espínola, Fernando
    et al.
    Centro Nacional Patagónico, Puerto Madryn, Argentina.
    Dionisi, Hebe M
    Centro Nacional Patagónico, Puerto Madryn, Argentina.
    Borglin, Sharon
    Lawrence Berkeley National Laboratory, Berkeley, USA.
    Brislawn, Colin J
    Pacific Northwest National Laboratory, Richland, USA.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Mac Cormack, Walter P
    Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina / Instituto Antártico Argentino, Buenos Aires, Argentina.
    Carroll, JoLynn
    UiT The Arctic University of Norway, Tromsø, Norway.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Lozada, Mariana
    Centro Nacional Patagónico, Puerto Madryn, Argentina.
    Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes2018Ingår i: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, nr 1, s. 123-139Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

  • 12. Glaser, Elzbieta
    et al.
    Eriksson, AnnaCarin
    Sjöling, Sara
    Bifunctional role of the bc1 complex in plants Mitochondrial bc1 complex catalyses both electron transport and protein processing1994Ingår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 346, nr 1, s. 83-87Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Abstract Nuclear  encoded  mitochondrial  precursor  proteins  are  cleaved  to  mature  size products  by the  general  mitochondrial  processing  peptidase  (MPP). In  contrast  to  non-plant  sources  where  MPP  is  a matrix  enzyme,  the  plant  mitochondrial  MPP  is localised  in  the  inner  membrane  and  constitutes an  integral  part  of  the  bc,  complex  of  the  respiratory  chain.  Core  proteins  of  the  complex  are  immunologically  related  and  show  high  sequence similarity  to the MPP  subunits  from  non-plant  sources.  The bc,  complex  in plants  is thus  bifunctional,  being  involved  both  in respiration  and  in protein processing

  • 13. Glaser, Elzbieta
    et al.
    Sjöling, Sara
    Determinants for processing by the mitochondrial processing peptidase (MPP) integrated into the cytochrome bc1 complex in plants1998Ingår i: Plant mitochondria: from gene to function : proceedings of the International congress on plant mitochondria: From gene to function, Aronsborg, Sweden, 22-27 June, 1998 / [ed] I.M. Møller, P. Gardeström, K. Glimelius, E. Glaser, Leiden: Backhuys , 1998, s. 231-236Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 14. Glaser, Elzbieta
    et al.
    Sjöling, Sara
    Szigyarto, Cristina
    Eriksson, AnnaCarin
    Plant mitochondrial protein import: precursor processing is catalysed by the integrated mitochondrial processing peptidase (MPP)/bc1 complex and degradation by the ATP-dependent proteinase1996Ingår i: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1275, nr 1-2, s. 33-37Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Several hundreds of mitochondrial proteins are nuclear encoded and are synthesised on cytosolic polyribosomes as precursor proteins. Most of these precursors contain an N-terminal extension called presequence which functions as targeting signal and which is cleaved off after import. Despite the fact that there are no sequence similarities and no consensus for the cleavage site in mitochondrial presequences, cleavage of almost all presequences is catalysed by a single, highly specific metalloendopeptidase, called general mitochondrial processing peptidase (MPP). MPP in plants is integrated into the bc1, complex of the respiratory chain and both subunits, α-MPP and β-MPP, are identical to the core proteins of the complex. Despite the fact that the bc1 complex in plants is bifunctional, catalysing bothelectron transport and protein processing, these two functions are distinct. MPP belongs to the Pitrilysin family of peptidases, characterised by a zinc binding motif, HXXEH74–76E, involved in catalysis. Both the membrane-bound integrated MPP/bc1 complex of plants and the soluble mammalian MPP recognise similar higher-order structural elements upstream from the cleavage site that are important for processing. The secondary structure with flexibility and stabilising elements, hydrofobicity, charge and length seem to influence the interaction with MPP. The newly imported non-assembled precursor inside mitochondria is degraded by a proteinase that is distinct from MPP or any other previously characterised proteinases, a novel ATP-dependent, membrane-associated serine-type proteinase.

  • 15. Glaser, Elzbieta
    et al.
    Sjöling, Sara
    Södertörns högskola, Avdelning Naturvetenskap.
    Tanudji, Marcel
    Södertörns högskola, Avdelning Naturvetenskap.
    Whelan, James
    Mitochondrial protein import in plants: Signals, Sorting, Targeting, Processing and Regulation1998Ingår i: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 38, nr 1-2, s. 311-338Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar genomes and specific intracellular protein trafficking, processing and assembly machinery. Mostmitochondrial proteins are synthesised as precursor proteins containing an N-terminal extension which functions as a targeting signal, which is proteolytically cleaved off after import into mitochondria. We review our present knowledge on components and mechanisms involved in the mitochondrial proteinimport process in plants. This encompasses properties of targeting peptides, sorting of precursor proteinsbetween mitochondria and chloroplasts, signal recognition, mechanism of translocation across the mitochondrial membranes and the role of cytosolic and organellar molecular chaperones in this process. The mitochondrial protein processing in plants is catalysed by the mitochondrial processing peptidase (MPP), which in contrast to other sources, is integrated into the bc1 complex of the respiratory chain. This is the most studied component of the plant import machinery characterised to date. What are the biochemical consequences of the integration of the MPP into an oligomeric protein complex and how are several hundred presequences of precursor proteins with no sequence similarities and no consensus for cleavage, specifically cleaved off by MPP? Finally we will address the emerging area of the control of protein import into mitochondria.

  • 16.
    Hjort, Karin
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Bergström, Maria
    Adesina, Modupe F.
    Jansson, Janet K.
    Smalla, Kornelia
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil2010Ingår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 71, nr 2, s. 197-207Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF103 of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  • 17.
    Hjort, Karin
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi. Uppsala University.
    Presti, Ilaria
    University of Insubria, Varese, Italy.
    Elväng, Annelie
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Marinelli, Flavia
    University of Insubria, Varese, Italy.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics2014Ingår i: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 98, nr 6, s. 2819-2828Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plant disease caused by fungal pathogens results in vast crop damage globally. Microbial communities of soil that is suppressive to fungal crop disease provide a source for the identification of novel enzymes functioning as bioshields against plant pathogens. In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome. We identified a novel bacterial chitinase, Chi18H8, with antifungal activity against several important crop pathogens. Sequence analyses show that the chi18H8 gene encodes a 425-amino acid protein of 46 kDa with an N-terminal signal peptide, a catalytic domain with the conserved active site F175DGIDIDWE183, and a chitinase insertion domain. Chi18H8 was expressed (pGEX-6P-3 vector) in Escherichia coli and purified. Enzyme characterization shows that Chi18H8 has a prevalent chitobiosidase activity with a maximum activity at 35 °C at pH lower than 6, suggesting a role as exochitinase on native chitin. To our knowledge, Chi18H8 is the first chitinase isolated from a metagenome library obtained in pure form and which has the potential to be used as a candidate agent for controlling fungal crop diseases. Furthermore, Chi18H8 may also answer to the demand for novel chitin-degrading enzymes for a broad range of other industrial processes and medical purposes.

  • 18.
    Hårdeman, Fredrik
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Pérez-Bercoff, Åsa
    University of Dublin, Dublin, Ireland.
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Comparative structure modelling and mutational analysis of the low-temperature-active metagenomically derived lipase h1Lip1Manuskript (preprint) (Övrigt vetenskapligt)
  • 19.
    Hårdeman, Fredrik
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institute.
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment2007Ingår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 59, nr 2, s. 524-534Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A novel lipase was isolated from a metagenomic library of Baltic Sea sediment bacteria. Prokaryotic DNA was extracted and cloned into a copy control fosmid vector (pCC1FOS) generating a library of > 7000 clones with inserts of 24-39 kb. Screening for clones expressing lipolytic activity based on the hydrolysis of tributyrin and p-nitrophenyl esters, identified 1% of the fosmids as positive. An insert of 29 kb was fragmented and subcloned. Subclones with lipolytic activity were sequenced and an open reading frame of 978 bp encoding a 35.4-kDa putative lipase/esterase h1Lip1 (DQ118648) with 54% amino acid similarity to a Pseudomomas putida esterase (BAD07370) was identified. Conserved regions, including the putative active site, GDSAG, a catalytic triad (Ser148, Glu242 and His272) and a HGG motif, were identified. The h1Lip1 lipase was over expressed, (pGEX-6P-3 vector), purified and shown to hydrolyse p-nitrophenyl esters of fatty acids with chain lengths up to C-14. Hydrolysis of the triglyceride derivative 1,2-di-O-lauryl-rac-glycero-3-glutaric acid 6'-methylresorufin ester (DGGR) confirmed that h1Lip1 was a lipase. The apparent optimal temperature for h1Lip1, by hydrolysis of p-nitrophenyl butyrate, was 35 degrees C. Thermal stability analysis showed that h1Lip1 was unstable at 25 degrees C and inactivated at 40 degrees C with t(1/2) < 5 min.

  • 20. Knorpp, Carina
    et al.
    Hugosson, Marie
    Sjöling, Sara
    Eriksson, AnnaCarin
    Glaser, Elzbieta
    Tissue-specific differences of the mitochondrial protein import machinery: in vitro import, processing and degradation of the pre-F1β subunit of the ATP synthase in spinach leaf and root mitochondria1994Ingår i: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 26, nr 2, s. 571-579Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study we report the first comparison of the mitochondrial protein import and processing events in two different tissues from the same organism. Both spinach leaf and root mitochondria were able to import and process the in vitro transcribed and translated Neurospora crassa F1 subunit of ATP synthase to the mature size product. Temperature optimum for protein import, 20 °C, was considerably lower than that found in other systems. In spinach leaf mitochondria, the processing peptidase has been shown to constitute an integral part of the bc1 complex of the respiratory chain. In accordance with these results, the majority of the processing activity in root mitochondria was also localized in the membrane. However, although the same amount of the processing peptidase was present per mg of membrane protein in both leaf and root mitochondria, as determined immunologically, the specific processing activity was several-fold higher in roots. Furthermore, in contrast to the processing enzyme in leaf, a portion of the processing activity could be disassociated from the root membrane with relatively weak salt treatment. The processing event in both the leaf and root membranes was always accompanied by a degradation of the F1 precursor. The degradation activity was found to be several-fold higher in roots than in leaves and was also partially dissociated from the membrane after salt treatment. Both the processing and degradation activities were inhibited by orthophenanthroline, a known metalloprotease inhibitor. These results show tissue-specific differencies of the processing event catalyzed by the bc1 complex and indicate the presence of two populations of the processing peptidase in root mitochondria.

  • 21.
    Lugomela, Charles
    et al.
    Department of Aquatic Sciences and Fisheries, University of Dar es Salaam, PO Box 35064 Dar es Salaam, Tanzania.
    Lyimo, Thomas J.
    Department of Molecular Biology and Biotechnology, University of Dar es Salaam, PO Box 35179, Dar es Salaam, Tanzania.
    Namkinga, Lucy A
    Department of Molecular Biology and Biotechnology, University of Dar es Salaam, PO Box 35179, Dar es Salaam, Tanzania.
    Moyo, Sabina
    Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, PO Box 65001 Dar es Salaam, Tanzania.
    Goericke, Ralph
    Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, 92093, USA.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Co-variation of Cholera with Climatic and Environmental Parameters in Coastal Regions of Tanzania2014Ingår i: Western Indian Ocean journal of marine science, ISSN 0856-860X, Vol. 13, nr 1, s. 93-105Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The bacterium causing cholera, Vibrio cholerae, is essentially a marine organism and its ecological dynamics have been linked to oceanographic conditions and climate. We used autoregressive models with external inputs to identify potential relationships between the number of cholera cases in the coastal regions of mainland Tanzania with climatic and environmental indices (maximum air temperature, sea surface temperature, wind speed and chlorophyll a). Results revealed that, between 2004 and 2010, coastal regions of mainland Tanzania inhabited by approximately 21% of the total population accounted for approximately 50% of the cholera cases and 40% of the total mortality. Significant co-variations were found between seasonally adjusted cholera cases and coastal ocean chlorophyll a and, to some degree, sea surface temperature, the outbreaks lagging behind by one to four months. Cholera cases in Dar es Salaam were also weakly related to the Indian Ocean Dipole Mode Index, lagging by five months, suggesting that it may be possible to predict cholera outbreaks for Dar es Salaam this period ahead. The results also suggest that the severity of cholera in coastal regions can be predicted by ocean conditions and that longer-term environmental and climate parameters may be used to predict cholera outbreaks along the coastal regions.

  • 22.
    López, J L
    et al.
    Universidad de Buenos Aires, Argentina.
    Golemba, M
    Hospital de Pediatría "Juan P. Garrahan", Argentina.
    Hernández, E
    UNSAM Campus Miguelete, Argentina / Universidad de Buenos Aires, Argentina.
    Lozada, M
    Centro Nacional Patagónico-CONICET, Argentina.
    Dionisi, H M
    Centro Nacional Patagónico-CONICET, Argentina.
    Jansson, J
    Pacific Northwest National Laboratory, Richland, WA, USA.
    Carroll, J
    UiT The Arctic University of Norway, Tromsø, Norway / Fram - High North Research Centre for Climate and the Environment, Tromsø, Norway.
    Lundgren, L
    Stockholm University.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Cormack, W P Mac
    UNSAM Campus Miguelete, Argentina / Universidad de Buenos Aires, Argentina.
    Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.2017Ingår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 93, nr 1, artikel-id fiw216Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis. Viral rhodopsin genes were homologues of Phaeocystis globosa virus and Organic lake Phycodnavirus Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus as well as Cryptophyta and Fungi. A re-screening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 aminoacids). Phylogeographic analysis revealed a geographycal clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsins (PAVR) genes related to Actinobacteria and Chloroflexi This is the first report about the existence of a phylogeographic association of the viral rhodopsins sequences from marine sediments.

  • 23.
    Matos, Marina N
    et al.
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Lozada, Mariana
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Anselmino, Luciano E
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Musumeci, Matías A
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Henrissat, Bernard
    Aix-Marseille Université, Marseille, France / INRA, Marseille, France / King Abdulaziz University, Jeddah, Saudi Arabia.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Mac Cormack, Walter P
    Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, Argentina / Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
    Carroll, JoLynn
    High North Research Centre for Climate and the Environment, Tromsø, Norway / UiT The Arctic University of Norway, Tromsø, Norway.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Lundgren, Leif
    Stockholm University.
    Dionisi, Hebe M
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments2016Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, nr 12, s. 4471-4484Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

  • 24.
    Musumeci, Matías A
    et al.
    Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Argentina.
    Lozada, Mariana
    Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Argentina.
    Rial, Daniela V
    Universidad Nacional de Rosario, CONICET, Rosario, Argentina.
    Mac Cormack, Walter P
    Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, Argentina / CONICET—Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Carroll, JoLynn
    Fram—High North Research Centre for Climate and the Environment, Tromsø, Norway / UiT The Arctic University of Norway, Tromsø, Norway.
    Dionisi, Hebe M
    Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Argentina.
    Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach2017Ingår i: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 15, nr 4, artikel-id 114Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.

  • 25. Ndaro, Simon G. M.
    et al.
    Sjöling, Sara
    Ólafsson, Emil
    Small-Scale Variation in Major Meiofaunal Taxa and Sediment Chemistry in Tropical Sediments1995Ingår i: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 24, nr 7/8, s. 470-474Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Variations in sediment biochemistry and abundance of meiofauna were investigated in three tropical habitats: mangrove forest, intertidal lagoon, and subtidal reef area in eastern Africa. Both the biochemical components of the pore water and the meiofauna varied substantially over small distances in all three habitats. In the mangrove area, the color of the pore water was found to be positively correlated with the major meiofaunal taxa, especially the nematodes. In the coastal lagoon, polychaetes showed negative correlation with particulate organic matter while other groups showed no correlation with any of the chemical components analyzed. In the subtidal reef area no chemical components were found to correlate with the meiofauna. When data from the three habitats are taken together two clear associations emerge. First, grain size shows a highly significant relationship with both total fauna and nematode numbers. Second, there is clear association between the amount of particulate organic carbon and particulate organic nitrogen in the pore water.

  • 26.
    Nesme, Joseph
    et al.
    Université de Lyon, Ecully, France / Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
    Achouak, Wafa
    Aix-Marseille Université, Saint-Paul-lez-Durance, France.
    Agathos, Spiros N
    Catholic University of Louvain, Louvain-la-Neuve, Belgium / Yachay Tech University, Urcuquí, Ecuador.
    Bailey, Mark
    Centre for Ecology and Hydrology, Oxford, UK.
    Baldrian, Petr
    Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic.
    Brunel, Dominique
    Centre National de Génotypage, Evry, France.
    Frostegård, Åsa
    Norwegian University of Life Sciences, Aas, Norway.
    Heulin, Thierry
    Aix-Marseille Université, Saint-Paul-lez-Durance, France.
    Jansson, Janet K
    Pacific Northwest National Laboratory, Richland, WA, USA.
    Jurkevitch, Edouard
    The Hebrew University of Jerusalem, Rehovot, Israel.
    Kruus, Kristiina L
    Technical Research Centre of Finland, Espoo, Finland.
    Kowalchuk, George A
    Utrecht University, Utrecht, Netherlands.
    Lagares, Antonio
    Universidad Nacional de La Plata, La Plata, Argentina.
    Lappin-Scott, Hilary M
    Swansea University, Swansea, UK.
    Lemanceau, Philippe
    Université de Bourgogne, Dijon, France.
    Le Paslier, Denis
    Université d'Evry Val d'Essonne, Evry, France.
    Mandic-Mulec, Ines
    University of Ljubljana, Ljubljana, Slovenia.
    Murrell, J Colin
    University of East Anglia, Norwich, UK.
    Myrold, David D
    Oregon State University, Corvallis, OR, USA.
    Nalin, Renaud
    NALINOV, Dremil Lafage, France.
    Nannipieri, Paolo
    University of Florence, Florence, Italy.
    Neufeld, Josh D
    University of Waterloo, Waterloo, ON, Canada.
    O'Gara, Fergal
    National University of Ireland, Cork, Ireland / Curtin University, Perth, WA, Australia.
    Parnell, John J
    National Ecological Observatory Network, Boulder, CO, USA.
    Pühler, Alfred
    Bielefeld University, Bielefeld, Germany.
    Pylro, Victor
    René Rachou Research Centre, Belo Horizonte, Brazil.
    Ramos, Juan L
    Consejo Superior de Investigaciones Científicas, Granada, Spain.
    Roesch, Luiz F W
    Federal University of Pampa, São Gabriel, Brazil.
    Schloter, Michael
    Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
    Schleper, Christa
    University of Vienna, Vienna, Austria.
    Sczyrba, Alexander
    Bielefeld University, Bielefeld, Germany.
    Sessitsch, Angela
    AIT Austrian Institute of Technology GmbH, Tulln, Austria.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Sørensen, Jan
    niversity of Copenhagen, Frederiksberg, Denmark.
    Sørensen, Søren J
    University of Copenhagen, Copenhagen, Denmark.
    Tebbe, Christoph C
    Thünen-Institute of Biodiversity, Braunschweig, Germany.
    Topp, Edward
    University of Western Ontario, London, ON, Canada.
    Tsiamis, George
    University of Patras, Agrinio, Greece.
    van Elsas, Jan Dirk
    University of Groningen, Groningen, Netherlands.
    van Keulen, Geertje
    Swansea University, Swansea, UK.
    Widmer, Franco
    Institute for Sustainability Sciences, Agroscope, Zürich, Switzerland.
    Wagner, Michael
    University of Vienna, Vienna, Austria.
    Zhang, Tong
    The University of Hong Kong, Hong Kong, China.
    Zhang, Xiaojun
    Shanghai Jiao Tong University, Shanghai, China.
    Zhao, Liping
    Shanghai Jiao Tong University, Shanghai, China.
    Zhu, Yong-Guan
    Chinese Academy of Sciences, Xiamen, China.
    Vogel, Timothy M
    Université de Lyon, Ecully, France.
    Simonet, Pascal
    Swansea University, Swansea, UK.
    Back to the Future of Soil Metagenomics2016Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, artikel-id 73Artikel i tidskrift (Refereegranskat)
  • 27.
    Saunders, Fred
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap. Södertörns högskola, Institutionen för livsvetenskaper, Geografi.
    Mohammed, Salim M.
    Jiddawi, Narriman
    Nordin, Karolina
    Lunden, Bengt
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper, Miljövetenskap.
    The changing social relations of a community-based mangrove forest project in Zanzibar2010Ingår i: Ocean and Coastal Management, ISSN 0964-5691, E-ISSN 1873-524X, Vol. 53, nr 4, s. 150-160Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Coastal areas in East Africa are experiencing rapid economic, resource management, demographic and technological shifts. In response diverse Community-based Natural Resource Management (CBNRM) applications have been embraced to provide mutual conservation and use benefits. These initiatives have met with mixed success in practice. Reflecting on the limitations of past research using common pool resources theory theory to study CBNRM we use insights from actor oriented theory combined with satellite image analysis to describe and discuss the forces dynamically influencing institutional and mangrove forest cover change at Kisakasaka, Zanzibar focussing on the formal CBNRM project period between 1996 and 2001, but also considering the period before and after this. We examine the shifting social relations that affected the performance and viability of the formal CBNRM arrangements. An integrated approach was taken to the presentation and discussion of results where it was possible to enrich and expand explanations of socio-environmental change, which was driven by a lack of government support, the undermining effects of party political divisions, and the lack of institutional adaptive capacity. We conclude that this was a useful approach to explain CBNRM intervention events at Kisakasaka.

  • 28.
    Saunders, Fred
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Mohammed, Salim M.
    Jiddawi, Narriman
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    An examination of governance arrangements at Kisakasaka mangrove reserve in Zanzibar2008Ingår i: Environmental Management, ISSN 0364-152X, E-ISSN 1432-1009, Vol. 41, nr 5, s. 663-675Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This study employs insights largely derived from critical reflections on the common pool resources (CPR) theory to examine the current governance arrangements in place to manage the mangrove forest at Kisakasaka, in Zanzibar, Tanzania. Kisakasaka was used as a site for a community-based management pilot project of forest resources in Zanzibar. After some initial success in setting up a local management structure and regulating access to the mangrove for mainly charcoal production, there are now clear indications that forest conditions have deteriorated dramatically with concomitant ongoing resource use problems for local villagers who have relied heavily on forest resources as a source of cash income. Extra-local factors, such as urban population increases and associated market pressures for charcoal, are also conjectured to overlay and interact with the institutional problems at Kisakasaka. As a result, over concern about the deterioration in the condition of the mangrove forest, the responsible government authority decided not to renew the community-based governance arrangements after an initial five-year pilot period. While revealing the inadequacies of existing governance arrangements and of its relationship to deteriorating forest conditions at Kisakasaka, this study concludes by suggesting an approach to more fully understand forces driving local resource management and use. 

  • 29. Schneider, Gisbert
    et al.
    Sjöling, Sara
    Wallin, Erik
    Wrede, Paul
    Glaser, Elzbieta
    von Heijne, Gunnar
    Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides1998Ingår i: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 30, nr 1, s. 49-60Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps, Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs, Neural networks were used to define local sequence features around precursor cleavage sites.

  • 30. Sjöling, Sara
    Identifying the benthic microbial community structure using a molecular technique2001Ingår i: Marine science development in Tanzania and eastern Africa: proceedings of the 20th Anniversary Conference on Advances in Marine Science in Tanzania, 28 June-1 July 1999, Zanzibar, Tanzania / [ed] Matthew D. Richmond, Julius Francis, Zanzibar, Tanzania: Institute of Marine Sciences, University of Dar es Salaam and Western Indian Ocean Marine Science Association , 2001, s. 233-238Konferensbidrag (Övrigt vetenskapligt)
  • 31.
    Sjöling, Sara
    et al.
    University College London, Gower St., London, United Kingdom .
    Cowan, D A
    High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica2003Ingår i: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 7, nr 4, s. 275-282Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The microbial diversity in maritime meltwater pond sediments from Bratina Island, Ross Sea, Antarctica was investigated by 16S rDNA-dependent molecular phylogeny. Investigations of the vertical distribution, phylogenetic composition, and spatial variability of Bacteria and Archaea in the sediment were carried out. Results revealed the presence of a highly diverse bacterial population and a significantly depth-related composition. Assessment of 173 partial 16S rDNA clones analyzed by amplified rDNA restriction analysis (ARDRA) using tetrameric restriction enzymes (HinP1I 5'GdelCGC3'and Msp I. 5'CdelCGG3', BioLabs) revealed 153 different bacterial OTUs (operational taxonomic units). However, only seven archaeal OTUs were detected, indicating low archaeal diversity. Based on ARDRA results, 30 bacterial clones were selected for sequencing and the sequenced clones fell into seven major lineages of the domain Bacteria; the alpha, gamma, and delta subdivisions of Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides, the Spirochaetaceae, and the Actinobacteria. All of the archaeal clones sequenced belonged to the group Crenarchaeota and phylogenetic analysis revealed close relationships with members of the deep-branching Group 1 Marine Archaea.

  • 32. Sjöling, Sara
    et al.
    Cowan, Don A
    Detecting human bacterial contamination in Antarctic soils2000Ingår i: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 23, nr 9, s. 644-650Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The presence of non-indigenous microbial contaminants resulting from human faecal contamination of old and currently occupied base and field camp sites in South Victoria Land, Antarctica, was assessed by PCR amplification of extracted soil DNA using species-specific PCR primers. Positive controls (samples recovered from the environs of Scott Base, including the sewage outfall) gave strong signals with Escherichia coli primers whereas Clostridium clostridiiforme primers yielded a signal only with the sewage outfall sample. A comparison was made of PCR amplification results from samples from the abandoned Canada Glacier camp site, the Lake Fryxell summer camp site, the Cape Bird Adelie penguin colony and pristine sites from relatively inaccessible regions of the Taylor Valley. Results indicated a possible residual level of E. coli contamination in the abandoned Canada Glacier camp site, but no significant contamination of the currently occupied Lake Fryxell camp site. These data may provide indirect evidence for improved awareness and standards of waste handling and disposal over the past two decades of Dry Valley field research.

  • 33.
    Sjöling, Sara
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Cowan, Don A
    University of the Western Cape, South Africa.
    Metagenomics: microbial community genomes revealed2008Ingår i: Psychrophiles: from biodiversity to biotechnology / [ed] Rosa Margesin, Franz Schinner, Jean-Claude Marx, Charles Gerday, Berlin, Heidelberg: Springer, 2008, s. 313-330Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    The rapidly expanding field of metagenomics has revolutionized the ability to analyzemicrobial communities by providing access to ‘true’ microbial diversity. This field has a broad range of applications in the areas of biodiversity, systems biology and biotechnology (Handelsman et al. 2002). As most microbial communities in soil, sediment or aquatic environments are highly complex, consisting of hundreds oreven thousands of species of which only a few have been cultured, the approaches collectively described as metagenomics, community genomics or environmental genomics have been developed to help to unlock this thus far hidden diversity. Metagenomics is therefore the application of modern genomic tools used to analyze the collective genomes of whole microbial communities (the metagenome) in an environmental sample, thereby bypassing the need for isolation or cultivation (Béjà et al. 2000; Riesenfeld et al. 2004b). Even though the tip of the microbial ice-berg has barely been scratched, this approach is rapidly increasing our knowledge of microbial genetic and functional diversity through gene/pathway discovery either by sequencing or activity-based screening strategies (Handelsman 2005).

  • 34.
    Sjöling, Sara
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Edlund, Anna
    Östersjöns döda bottnar fulla med liv2008Ingår i: HavsUtsikt, ISSN 1104-0513, nr 1, s. 12-13Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 35. Sjöling, Sara
    et al.
    Eriksson, AnnaCarin
    Glaser, Elzbieta
    A helical element in the C-terminal domain of the N. plumbaginifolia F1 beta presequence is important for recognition by the mitochondrial processing peptidase1994Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 269, nr 51, s. 32059-32062Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The mitochondrial processing peptidase (MPP) in lower eucaryots and mammals is a matrix enzyme, whereas MPP in plants constitutes an integral part of the bc1 complex of the respiratory chain. The isolated spinach leaf bc1 complex catalyzes cleavage of the precursor of Nicotiana plumbaginifolia F1 beta subunit of the ATP synthase, resulting in a production of mature protein and a presequence that consists of 54 amino acids. A synthetic peptide derived from the C-terminal part of the presequence, containing 17 amino acids with a helical structural element, p-F1 beta(38-54), was an efficient inhibitor of the processing, whereas a peptide derived from the N-terminal part of the presequence, p-F1 beta(1-18), was much less effective. ATIII, a helical peptide derived from antithrombin III, was not recognized by MPP. Synthetic peptides corresponding to 4, 6, and 11 amino acids of the C terminus of the presequence, p-F1 beta(51-54), p-F1 beta(49-54), and p-F1 beta(44-54) were almost completely inert. Competition studies show that MPP recognizes the C-terminal domain of the presequence rather than the N-terminal domain. Furthermore, the alpha-helical element of the C-terminal domain is shown to be required for the recognition event.

  • 36. Sjöling, Sara
    et al.
    Glaser, Elzbieta
    Mitochondrial Processing Peptidase integrated into the bc1 complex of the respiratory chain in Spinach.1997Ingår i: Proteolysis in Cell Functions / [ed] Hopsu-Havu, Väino K., Järvinen, Mikko, Kirschke, Heidrun, Amsterdam: IOS , 1997, s. 307-322Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 37. Sjöling, Sara
    et al.
    Glaser, Elzbieta
    Mitochondrial targeting peptides in plants1998Ingår i: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 3, nr 4, s. 136-140Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Proteins function at distinct sites in the cell, yet most are primarily synthesized in the cytosol and must therefore be transported intracellularly to their final destination. Mitochondrial targeting peptides are localized at the N-terminus of the precursor proteins and most are cleaved off after import into mitochondria. Cleavage is catalysed by the general mitochondrial processing peptidase, which, in plants, is integrated into the bc1 complex of the respiratory chain. This peptidase recognizes the cleavage sites of nearly 1000 precursor proteins that have no sequence similarity.

  • 38.
    Sjöling, Sara
    et al.
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Mohammed, S M
    Lyimo, T J
    Kyaruzi, J J
    Benthic bacterial diversity and nutrient processes in mangroves: impact of deforestation2005Ingår i: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 63, nr 3, s. 397-406Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The bacterial diversity and nutrient dynamics of mangrove sediments in Kisakasaka, Tanzania, was investigated in order to evaluate potential changes associated with deforestation of mangroves. Study sites included relatively undisturbed, recently protected mangroves and clear-cut mangrove areas that were sampled during both the wet and dry seasons. Physicochemical parameters, nitrogenase activity, pore water nutrient concentrations and bacterial diversity were measured in sediment depth profiles using both molecular and chemical techniques. Results show that there are significant differences in sediment pore water nutrient concentrations and bacterial diversity in sediments of mangrove areas which have been deforested compared to those which have been protected. Average measured values for protected and deforested areas, respectively, were: sulphide (S-2-),S- < 42 +/- 10 mu M and > 1.9 +/- 0.5 mM at 30 cm depth; ammonium (NH4+), 58 +/- 2 mu M and 113 +/- 12 mu M at 4-5 cm depth; soluble reactive phosphate, 40.2 +/- 11 mu M and 18.4 +/- 1.2 at 4-5 cm depth. Nitrogen fixation rates were lower in deforested areas during day and night, organic content was higher in protected areas (20 +/- 5%) compared to deforested areas (12 +/- 3%). The bacterial diversity was lower in deforested areas as determined by Shannon index using 16S rRNA gene analysis with terminal restriction fragment length polymorphism.

  • 39. Sjöling, Sara
    et al.
    Reyet, Raphael
    "Les Maasaï sont en train de perdre leurs terres"2002Ingår i: Les Maasaï: pays, histoire, économie, environnement, croyances, culture matérielle / [ed] Xavier van der Stappen, Tournai, Belgique: Renaissance du livre , 2002, s. 65-69Kapitel i bok, del av antologi (Övrig (populärvetenskap, debatt, mm))
  • 40.
    Sjöling, Sara
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Stafford, W
    Cowan, D A
    Soil metagenomics: exploring and exploiting the soil microbial gene pool2007Ingår i: Modern soil microbiology / [ed] Jan Dirk van Elsas, Janet K Jansson, Jack T Trevors, Boca Raton: CRC Press, Taylor & Francis , 2007, s. 409-434Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 41.
    Sjöling, Sara
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Thureborn, Petter
    Den gömda och okända rikedomen2009Ingår i: HavsUtsikt, ISSN 1104-0513, nr 3, s. 8-9Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 42.
    Sjöling, Sara
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Thureborn, Petter
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Livet i havets djup2016Ingår i: HavsUtsikt- Om havsmiljön och Svensk havsforskning, ISSN 1104-0513, nr 2, s. 16-18Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 43. Sjöling, Sara
    et al.
    Waltner, Mary
    Kalousek, Frantisek
    Glaser, Elzbieta
    Weiner, Henry
    Studies on Protein Processing for Membrane-Bound Spinach Leaf Mitochondrial Processing Peptidase Integrated into the Cytochrome bc1, Complex and the Soluble Rat Liver Matrix Mitochondrial Processing Peptidase1996Ingår i: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 242, nr 1, s. 114-121Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The plant mitochondrial processing peptidase (MPP) that catalyses the cleavage of the presequences from precursor proteins during or after protein import is a membrane-bound enzyme that constitutes an integral part of the bc1 complex of the respiratory chain. In contrast, MPP from mammals is soluble in the matrix space and does not form part of the respiratory chain. In the present study, we have compared the substrate specificity of the isolated spinach leaf bc1/MPP with rat liver MPP using synthetic signal peptides and different mitochondrial precursor proteins. Inhibition studies of processing with synthetic peptides showed a similar inhibition pattern for plant and rat MPP activity. A peptide derived from the presequence of rat liver mitochondrial aldehyde dehydrogenase (ALDH) was a potent inhibitor of the spinach and rat MPP. Two nonprocessed signal peptides, rhodanese and linker-deleted ALDH (a form of ALDH that lacks the RGP linker connecting two helices in the presequence) had lower inhibitory effects towards each protease. The signal peptide from thiolase, another nonprocessed protein, had little inhibitory effect on MPP. Peptides derived from presequence of the plant Nicotiana plumbaginifolia F1β also showed a similar inhibitory pattern with rat MPP as with spinach MPP processing. In-vitro synthesised precursors of plant N. plumbaginifolia F1β and rat liver ALDH were cleaved to mature form by both spinach and rat MPP. However, the efficiency of processing was higher with the homologous precursor. Linker-deleted ALDH, rhodanese, and thiolase were not processed by the mammalian or plant MPP. However, both forms of MPP cleaved a mutated form of rhodanese that possesses a typical MPP cleavage motif, RXY S. Addition of the same cleavage motif to thiolase did not result in processing by either MPP. These results show that similar higher-order structural elements upstream from the cleavage site are important for processing by both the membrane-bound plant and the soluble mammalian MPP.

  • 44. Tanudji, Marcel
    et al.
    Sjöling, Sara
    Glaser, Elzbieta
    Whelan, James
    Signals Required for the Import and Processing of the Alternative Oxidase into Mitochondria1999Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 274, s. 1286-1293Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The critical residues involved in targeting and processing of the soybean alternative oxidase to plant and animal mitochondria was investigated. Import of various site-directed mutants into soybean mitochondria indicated that positive residues throughout the length of the presequence were important for import, not just those in the predicted region of amphiphilicity. The position of the positive residues in the C-terminal end of the presequence was also important for import. Processing assays of the various constructs with purified spinach mitochondrial processing peptidase showed that all the −2-position mutants had a drastic effect on processing. In contrast to the import assay, the position of the positive residue could be changed for processing. Deletion mutants confirmed the site-directed mutagenesis data in that an amphiphilic α-helix was not the only determinant of mitochondrial import in this homologous plant system. Import of these constructs into rat liver mitochondria indicated that the degree of inhibition differed and that the predicted region of amphiphilic α-helix was more important with rat liver mitochondria. Processing with a rat liver matrix fraction showed little inhibition. These results are discussed with respect to targeting specificity in plant cells and highlight the need to carry out homologous studies and define the targeting requirements to plant mitochondria.

  • 45. Thompson, Luke R.
    et al.
    Sanders, Jon G.
    McDonald, Daniel
    Amir, Amnon
    Ladau, Joshua
    Locey, Kenneth J.
    Prill, Robert J.
    Tripathi, Anupriya
    Gibbons, Sean M.
    Ackermann, Gail
    Navas-Molina, Jose A.
    Janssen, Stefan
    Kopylova, Evguenia
    Vázquez-Baeza, Yoshiki
    González, Antonio
    Morton, James T.
    Mirarab, Siavash
    Zech Xu, Zhenjiang
    Jiang, Lingjing
    Haroon, Mohamed F.
    Kanbar, Jad
    Zhu, Qiyun
    Jin Song, Se
    Kosciolek, Tomasz
    Bokulich, Nicholas A.
    Lefler, Joshua
    Brislawn, Colin J.
    Humphrey, Gregory
    Owens, Sarah M.
    Hampton-Marcell, Jarrad
    Berg-Lyons, Donna
    McKenzie, Valerie
    Fierer, Noah
    Fuhrman, Jed A.
    Clauset, Aaron
    Stevens, Rick L.
    Shade, Ashley
    Pollard, Katherine S.
    Goodwin, Kelly D.
    Jansson, Janet K.
    Gilbert, Jack A.
    Knight, Rob
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Zhao, Hongxia
    A communal catalogue reveals Earth’s multiscale microbial diversity2017Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 551, s. 457-463Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

  • 46.
    Thureborn, Petter
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Franzetti, Andrea
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. University of Milano-Bicocca, Milano, Italy.
    Lundin, Daniel
    Science for Life Laboratories / Linnéuniversitetet.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Biologi.
    Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments2016Ingår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, artikel-id e1593Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning.

  • 47.
    Thureborn, Petter
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Hu, Yue O. O.
    KTH.
    Franzetti, Andrea
    University of Milano-Bicocca, Milano, Italy.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Lundin, Daniel
    Linnaeus University.
    A dark, anoxic mausoleum for DNA: perceived and actual community structure in the Landsort Deep sediment, the Baltic Sea2016Ingår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.

  • 48.
    Thureborn, Petter
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap. Stockholm University.
    Lundin, Daniel
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik. KTH & Stockholm University.
    Plathan, Josefin
    Stockholm University.
    Poole, Anthony M
    School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
    Sjöberg, Britt-Marie
    Stockholm University.
    Sjöling, Sara
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities2013Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 9, artikel-id e74983Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Baltic Sea is characterized by hyposaline surface waters, hypoxic and anoxic deep waters and sediments. These conditions, which in turn lead to a steep oxygen gradient, are particularly evident at Landsort Deep in the Baltic Proper. Given these substantial differences in environmental parameters at Landsort Deep, we performed a metagenomic census spanning surface to sediment to establish whether the microbial communities at this site are as stratified as the physical environment. We report strong stratification across a depth transect for both functional capacity and taxonomic affiliation, with functional capacity corresponding most closely to key environmental parameters of oxygen, salinity and temperature.

    We report similarities in functional capacity between the hypoxic community and hadal zone communities, underscoring the substantial degree of eutrophication in the Baltic Proper. Reconstruction of the nitrogen cycle at Landsort deep shows potential for syntrophy between archaeal ammonium oxidizers and bacterial denitrification at anoxic depths, while anaerobic ammonium oxidation genes are absent, despite substantial ammonium levels below the chemocline. Our census also reveals enrichment in genetic prerequisites for a copiotrophic lifestyle and resistance mechanisms reflecting adaptation to prevalent eutrophic conditions and the accumulation of environmental pollutants resulting from ongoing anthropogenic pressures in the Baltic Sea.

  • 49. van Elsas, Jan Dirk
    et al.
    Costal, Rodrigo
    Jansson, Janet
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Bailey, Mark
    Nalin, Renaud
    Vogel, Timothy M.
    van Overbeek, Leo
    The metagenomics of disease-suppressive soils - experiences from the METACONTROL project2008Ingår i: Trends in Biotechnology, ISSN 0167-7799, E-ISSN 1879-3096, Vol. 26, nr 11, s. 591-601Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Soil teems with microbial genetic information that can be exploited for biotechnological innovation. Because only a fraction of the soil microbiota is cultivable, our ability to unlock this genetic complement has been hampered. Recently developed molecular tools, which make it possible to utilize genomic DNA from soil, can bypass cultivation and provide information on the collective soil metagenome with the aim to explore genes that encode functions of key interest to biotechnology. The metagenome of disease-suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging. Here, we examine crucial issues and challenges that so far have hindered the metagenomic exploration of soil by drawing on experience from a trans-European project on disease-suppressive soils denoted METACONTROL.

  • 50. Zhang, X P
    et al.
    Sjöling, Sara
    Tanudji, M
    Somogyi, L
    Andreu, D
    Eriksson, L E G
    Graslund, Z
    Whelan, J
    Glaser, E
    Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase2001Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 27, nr 5, s. 427-438Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing peptidase (MPP) have been investigated using mutagenesis and bioinformatics approaches. All plant mitochondrial presequences with a cleavage site that was confirmed by experimental studies can be grouped into three classes. Two major classes contain an arginine residue at position -2 or -3, and the third class does not have any conserved arginines. Sequence logos revealed loosely conserved cleavage motifs for the first two classes but no significant amino acid conservation for the third class. Investigation of processing determinants for a class III precursor, Nicotiana plumbaginifolia F(1)beta precursor of ATP synthase (pF(1)beta), was performed using a series of pF(1)beta presequence mutants and mutant presequence peptides derived from the C-terminal portion of the presequence. Replacement of -2 Gln by Arg inhibited processing, whereas replacement of either the most proximally located -5 Arg or -15 Arg by Leu had only a low inhibitory effect. The C-terminal portion of the pF(1)beta presequence forms a helix-turn-helix structure. Mutations disturbing or prolonging the helical element upstream of the cleavage site inhibited processing significantly. Structural models of potato MPP and the C-terminal pF(1)beta presequence peptide were built by homology modelling and empirical conformational energy search methods, respectively. Molecular docking of the pF(1)beta presequence peptide to the MPP model suggested binding of the peptide to the negatively charged binding cleft formed by the alpha -MPP and beta -MPP subunits in close proximity to the H111XXE114H115X(116-190)E191 proteolytic active site on beta -MPP. Our results show for the first time that the amino acid at the -2 position, even if not an arginine, as well as structural properties of the C-terminal portion of the presequence are important determinants for the processing of a class III precursor by MPP.

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